The 28-year-old scored twice in the first half before adding a fine third just after the break as the Gunners romped to a 4-1 victory in their final group game in Switzerland.
Wenger was delighted with the poacher's instinct shown by a player who has struggled to find fitness and a place in Arsenal's first-team plans since joining from Deportivo La Coruna in August.
"I think Perez took advantage of the fact we created good chances," he told BT Sport. "He is a goalscorer you know, he has shown he has a good smell for the goal."
And although Wenger is wary of anticipating an easier draw in the last 16, he admits he can feel "a little less guilty" about facing a tougher opponent given that they will play the second leg of the tie at home.
"It is difficult to know but you feel a bit less guilty if you have a bad draw if first than second - we have done our job and let's see what happens," he said.
"I thought Ludogorets were a good side - they got a great result that helps us top the group, which was what we wanted.
"We did the job in a convincing way, we were mobile and overall had a committed performance."
Defender Laurent Koscielny insisted Arsenal had not given up hope of finishing top even after their draw at home to PSG handed the French champions the advantage.
"We had a small chance to finish first," he said. "After PSG last time we said we had one more game, we did our job and PSG did not.
"It is important to finish first because we have a second game at home but we will have a big team so we will see who we get in the draw."